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Zhang Y, Mo Y, Li J, Liu L, Gao Y, Zhang Y, Huang Y, Ren L, Zhu H, Jiang X, Ling Y. Divergence in regulatory mechanisms of GR-RBP genes in different plants under abiotic stress. Sci Rep 2024; 14:8743. [PMID: 38627506 PMCID: PMC11021534 DOI: 10.1038/s41598-024-59341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
The IVa subfamily of glycine-rich proteins (GRPs) comprises a group of glycine-rich RNA binding proteins referred to as GR-RBPa here. Previous studies have demonstrated functions of GR-RBPa proteins in regulating stress response in plants. However, the mechanisms responsible for the differential regulatory functions of GR-RBPa proteins in different plant species have not been fully elucidated. In this study, we identified and comprehensively studied a total of 34 GR-RBPa proteins from five plant species. Our analysis revealed that GR-RBPa proteins were further classified into two branches, with proteins in branch I being relatively more conserved than those in branch II. When subjected to identical stresses, these genes exhibited intensive and differential expression regulation in different plant species, corresponding to the enrichment of cis-acting regulatory elements involving in environmental and internal signaling in these genes. Unexpectedly, all GR-RBPa genes in branch I underwent intensive alternative splicing (AS) regulation, while almost all genes in branch II were only constitutively spliced, despite having more introns. This study highlights the complex and divergent regulations of a group of conserved RNA binding proteins in different plants when exposed to identical stress conditions. These species-specific regulations may have implications for stress responses and adaptations in different plant species.
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Affiliation(s)
- Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yanhu Gao
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hongbo Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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Ahmed S, Khan MSS, Xue S, Islam F, Ikram AU, Abdullah M, Liu S, Tappiban P, Chen J. A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato. HORTICULTURE RESEARCH 2024; 11:uhae014. [PMID: 38464477 PMCID: PMC10923648 DOI: 10.1093/hr/uhae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/09/2024] [Indexed: 03/12/2024]
Abstract
Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.
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Affiliation(s)
- Sulaiman Ahmed
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | | | - Songlei Xue
- Jiangsu Coastal Area Institute of Agricultural Sciences, Yancheng 224000, China
| | - Faisal Islam
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Aziz Ul Ikram
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minghang, 200240, Shanghai, China
| | - Shan Liu
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
| | - Piengtawan Tappiban
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Jian Chen
- International Genome Center, Jiangsu University, Zhenjiang 212013, China
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Li J, Zhao R, Liu J, Yao J, Ma S, Yin K, Zhang Y, Liu Z, Yan C, Zhao N, Zhou X, Chen S. Populus euphratica GRP2 Interacts with Target mRNAs to Negatively Regulate Salt Tolerance by Interfering with Photosynthesis, Na +, and ROS Homeostasis. Int J Mol Sci 2024; 25:2046. [PMID: 38396725 PMCID: PMC10888501 DOI: 10.3390/ijms25042046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The transcription of glycine-rich RNA-binding protein 2 (PeGRP2) transiently increased in the roots and shoots of Populus euphratica (a salt-resistant poplar) upon initial salt exposure and tended to decrease after long-term NaCl stress (100 mM, 12 days). PeGRP2 overexpression in the hybrid Populus tremula × P. alba '717-1B4' (P. × canescens) increased its salt sensitivity, which was reflected in the plant's growth and photosynthesis. PeGRP2 contains a conserved RNA recognition motif domain at the N-terminus, and RNA affinity purification (RAP) sequencing was developed to enrich the target mRNAs that physically interacted with PeGRP2 in P. × canescens. RAP sequencing combined with RT-qPCR revealed that NaCl decreased the transcripts of PeGRP2-interacting mRNAs encoding photosynthetic proteins, antioxidative enzymes, ATPases, and Na+/H+ antiporters in this transgenic poplar. Specifically, PeGRP2 negatively affected the stability of the target mRNAs encoding the photosynthetic proteins PETC and RBCMT; antioxidant enzymes SOD[Mn], CDSP32, and CYB1-2; ATPases AHA11, ACA8, and ACA9; and the Na+/H+ antiporter NHA1. This resulted in (i) a greater reduction in Fv/Fm, YII, ETR, and Pn; (ii) less pronounced activation of antioxidative enzymes; and (iii) a reduced ability to maintain Na+ homeostasis in the transgenic poplars during long-term salt stress, leading to their lowered ability to tolerate salinity stress.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Rui Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Jian Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Jun Yao
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, China;
| | - Siyuan Ma
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Kexin Yin
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Ying Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Zhe Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Caixia Yan
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Nan Zhao
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Xiaoyang Zhou
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
| | - Shaoliang Chen
- State Key Laboratory of Efficient Production of Forest Resources, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China; (J.L.); (R.Z.); (J.L.); (S.M.); (K.Y.); (Y.Z.); (Z.L.); (C.Y.); (N.Z.); (X.Z.)
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Chandra AK, Pandey D, Sood S, Joshi DC, Tiwari A, Sharma D, Gururani K, Kumar A. Uncovering the genomic regions underlying grain iron and zinc content using genome-wide association mapping in finger millet. 3 Biotech 2024; 14:47. [PMID: 38268987 PMCID: PMC10803704 DOI: 10.1007/s13205-023-03889-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/14/2023] [Indexed: 01/26/2024] Open
Abstract
Finger millet, being rich source of essential minerals like iron and zinc, is an ideal model to identify candidate genes contributing to high grain iron content (GIC) and zinc content (GZC) in plants. Hence, finger millet diversity panel comprised of 202 genotypes was evaluated in two geographical locations and found to have a wide variation for GIC and GZC. A genome-wide association study using 2977 single nucleotide polymorphism (SNP) markers identified reliable marker-trait associations (MTAs). The use of general linear model (GLM) and mixed linear model (MLM) approaches revealed 5 and 8 common MTAs linked to GIC and GZC, respectively, for both Almora and Pantnagar locations, with a high level of significance (P < 0.01). However, 12 significant MTAs were found to be linked with GIC for Pantnagar location alone. The MTAs were associated with specific genes that produce ferritin (Fer1), iron-regulated transporter-like protein (IRT2), and yellow stripe-like 2 proteins (YSL2). These genes are likely linked to GIC variation in finger millet. Additionally, the variation in GZC in finger millet was connected to genes that encode zinc transporters, namely ZIP1 protein (ZIP1) and ZTP29-like protein (ZTP29). Compared to low GIC and GZC genotypes, high GIC and GZC genotypes exhibited greater relative expression of these genes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03889-1.
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Affiliation(s)
- Ajay Kumar Chandra
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Salej Sood
- Crop Improvement Division, Central Potato Research Institute, Shimla, Himachal Pradesh 171001 India
| | - Dinesh Chandra Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand 263601 India
| | - Apoorv Tiwari
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Computer Science and Information Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh 211007 India
| | - Divya Sharma
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Botany, Delhi University, North Campus, Delhi, 110007 India
| | - Kavita Gururani
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
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5
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Liu Z, Zhang T, Xu R, Liu B, Han Y, Dong W, Xie Q, Tang Z, Lei X, Wang C, Fu Y, Gao C. BpGRP1 acts downstream of BpmiR396c/BpGRF3 to confer salt tolerance in Betula platyphylla. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:131-147. [PMID: 37703500 PMCID: PMC10754015 DOI: 10.1111/pbi.14173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 07/22/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023]
Abstract
Glycine-rich RNA-binding proteins (GRPs) have been implicated in the responses of plants to environmental stresses, but the function of GRP genes involved in salt stress and the underlying mechanism remain unclear. In this study, we identified BpGRP1 (glycine-rich RNA-binding protein), a Betula platyphylla gene that is induced under salt stress. The physiological and molecular responses to salt tolerance were investigated in both BpGRP1-overexpressing and suppressed conditions. BpGRF3 (growth-regulating factor 3) was identified as a regulatory factor upstream of BpGRP1. We demonstrated that overexpression of BpGRF3 significantly increased the salt tolerance of birch, whereas the grf3-1 mutant exhibited the opposite effect. Further analysis revealed that BpGRF3 and its interaction partner, BpSHMT, function upstream of BpGRP1. We demonstrated that BpmiR396c, as an upstream regulator of BpGRF3, could negatively regulate salt tolerance in birch. Furthermore, we uncovered evidence showing that the BpmiR396c/BpGRF3 regulatory module functions in mediating the salt response by regulating the associated physiological pathways. Our results indicate that BpmiR396c regulates the expression of BpGRF3, which plays a role in salt tolerance by targeting BpGRP1.
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Affiliation(s)
- Zhongyuan Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
- Key Laboratory of Forest Plant EcologyMinistry of EducationNortheast Forestry UniversityHarbinChina
- College of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbinChina
| | - Tengqian Zhang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Ruiting Xu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Baichao Liu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Yating Han
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Wenfang Dong
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Qingjun Xie
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Zihao Tang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Xiaojin Lei
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Chao Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Yujie Fu
- Key Laboratory of Forest Plant EcologyMinistry of EducationNortheast Forestry UniversityHarbinChina
- College of ChemistryChemical Engineering and Resource UtilizationNortheast Forestry UniversityHarbinChina
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
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Hu Y, Dai Z, Huang J, Han M, Wang Z, Jiao W, Gao Z, Liu X, Liu L, Ma Z. Genome-wide identification and expression analysis of the glutamate receptor gene family in sweet potato and its two diploid relatives. FRONTIERS IN PLANT SCIENCE 2023; 14:1255805. [PMID: 38179475 PMCID: PMC10764598 DOI: 10.3389/fpls.2023.1255805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024]
Abstract
Plant glutamate receptor (GLR) homologs are crucial calcium channels that play an important role in plant development, signal transduction, and response to biotic and abiotic stresses. However, the GLR gene family has not yet been thoroughly and systematically studied in sweet potato. In this study, a total of 37 GLR genes were identified in the cultivated hexaploid sweet potato (Ipomoea batatas), and 32 GLR genes were discovered in each of the two diploid relatives (Ipomoea trifida and Ipomoea triloba) for the first time. Based on their evolutionary relationships to those of Arabidopsis, these GLRs were split into five subgroups. We then conducted comprehensive analysis to explore their physiological properties, protein interaction networks, promoter cis-elements, chromosomal placement, gene structure, and expression patterns. The results indicate that the homologous GLRs of the cultivated hexaploid sweet potato and its two relatives are different. These variations are reflected in their functions related to plant growth, hormonal crosstalk, development of tuberous roots, resistance to root rot, and responses to abiotic stress factors, all of which are governed by specific individual GLR genes. This study offers a comprehensive analysis of GLR genes in sweet potato and its two diploid relatives. It also provides a theoretical basis for future research into their regulatory mechanisms, significantly influencing the field of molecular breeding in sweet potatoes.
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Affiliation(s)
- Yaya Hu
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhuoru Dai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
| | - Jinan Huang
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Meikun Han
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhiwei Wang
- Department of Agriculture Forestry and Biological Engineering, Baoding Vocational and Technical College, Baoding, Hebei, China
| | - Weijing Jiao
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhiyuan Gao
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Xinliang Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Lanfu Liu
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhimin Ma
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
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Duan M, Zong M, Guo N, Han S, Wang G, Miao L, Liu F. Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea. PLANTS (BASEL, SWITZERLAND) 2023; 12:3706. [PMID: 37960062 PMCID: PMC10649936 DOI: 10.3390/plants12213706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants.
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Affiliation(s)
- Mengmeng Duan
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Mei Zong
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Ning Guo
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Shuo Han
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Guixiang Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
| | - Liming Miao
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China;
| | - Fan Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing 100097, China; (M.D.); (M.Z.); (N.G.); (S.H.); (G.W.)
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8
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Cheng K, Zhang C, Lu Y, Li J, Tang H, Ma L, Zhu H. The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3504. [PMID: 37836244 PMCID: PMC10575402 DOI: 10.3390/plants12193504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
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Affiliation(s)
- Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hui Tang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
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9
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Dai Z, Yan P, He S, Jia L, Wang Y, Liu Q, Zhai H, Zhao N, Gao S, Zhang H. Genome-Wide Identification and Expression Analysis of SWEET Family Genes in Sweet Potato and Its Two Diploid Relatives. Int J Mol Sci 2022; 23:ijms232415848. [PMID: 36555491 PMCID: PMC9785306 DOI: 10.3390/ijms232415848] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Sugar Will Eventually be Exported Transporter (SWEET) proteins are key transporters in sugar transportation. They are involved in the regulation of plant growth and development, hormone crosstalk, and biotic and abiotic stress responses. However, SWEET family genes have not been explored in the sweet potato. In this study, we identified 27, 27, and 25 SWEETs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These SWEETs were divided into four subgroups according to their phylogenetic relationships with Arabidopsis. The protein physiological properties, chromosome localization, phylogenetic relationships, gene structures, promoter cis-elements, protein interaction networks, and expression patterns of these 79 SWEETs were systematically investigated. The results suggested that homologous SWEETs are differentiated in sweet potato and its two diploid relatives and play various vital roles in plant growth, tuberous root development, carotenoid accumulation, hormone crosstalk, and abiotic stress response. This work provides a comprehensive comparison and furthers our understanding of the SWEET genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potato.
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Affiliation(s)
- Zhuoru Dai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Pengyu Yan
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
| | - Licong Jia
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai 265500, China
| | - Yannan Wang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Hong Zhai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ning Zhao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Shaopei Gao
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute, China Agricultural University, Sanya 572025, China
- Correspondence: ; Tel./Fax: +86-010-6273-2559
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10
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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11
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Integrated Analysis of Metabolome and Transcriptome Reveals the Difference in Flavonoid Biosynthesis between the Red- and White-Sarcocarp Pomelo Fruits. Metabolites 2022; 12:metabo12121161. [PMID: 36557200 PMCID: PMC9782486 DOI: 10.3390/metabo12121161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Flavonoids are bioactive secondary metabolites that play multiple roles in plants. However, studies on the flavonoid accumulation of the pomelo fruit are rare. In this study, we conducted a widely targeted metabolome analysis by using ultra-performance liquid chromatography and tandem mass spectrometry and identified 550 metabolites in the sarcocarp from red (C. maxima Merr. var. Tubtim Siam) and white pomelos (C. maxima (Burm.) Osbeck). A total of 263 significantly changed metabolites were detected from the 550 metabolites. Content analysis of the significantly changed metabolites (SCMs) showed that 138 SCMs were highly accumulated, whereas 125 SCMs were observed with lower content in red-sarcocarp pomelo. Importantly, 103 of the 263 SCMs were flavonoids, including 34 flavonoids, 29 flavonols, 18 flavonoid carbonosides, 9 dihydroflavones, 6 isoflavones, 5 anthocyanins, 1 dihydroflavonol, and 1 chalcone. Gene ontology analysis indicated that upregulated genes in red-sarcocarp pomelo were significantly enriched in GO terms related to flavonoids including flavonoid biosynthetic processes. Several important differentially expressed genes were detected in the correlation network, especially Cg2g009540 which is an orthologous gene of AtCHS, also detected in flavonoid biosynthesis networks, and which could be related to the high level of total flavonoids in the red-sarcocarp pomelo. Our study demonstrated the fluctuation of flavonoid biosynthesis in the two pomelo cultivars and laid a theoretical foundation for pomelo breeding to generate fruits with a high flavonoid content.
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12
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Singh RV, Sambyal K. β-galactosidase as an industrial enzyme: production and potential. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02507-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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13
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Yang Z, Dong T, Dai X, Wei Y, Fang Y, Zhang L, Zhu M, Nawaz G, Cao Q, Xu T. Comparative Analysis of Salt Responsive MicroRNAs in Two Sweetpotato [ Ipomoea batatas (L.) Lam.] Cultivars With Different Salt Stress Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:879819. [PMID: 35874022 PMCID: PMC9302446 DOI: 10.3389/fpls.2022.879819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Sweetpotato [Ipomoea batatas (L.) Lam.] is an important food, vegetable and economic crop, but its productivity is remarkably affected by soil salinity. MiRNAs are a class of endogenous non-coding small RNAs that play an important role in plant resistance to salt stress. However, the function of miRNAs still remains largely unknown in sweetpotato under salt stress. Previously, we identified salt-responsive miRNAs in one salt-sensitive sweetpotato cultivar "Xushu 32." In this study, we identified miRNAs in another salt-tolerant cultivar "Xushu 22" by high-throughput deep sequencing and compared the salt-responsive miRNAs between these two cultivars with different salt sensitivity. We identified 687 miRNAs in "Xushu 22," including 514 known miRNAs and 173 novel miRNAs. Among the 759 miRNAs from the two cultivars, 72 and 109 miRNAs were specifically expressed in "Xushu 32" and "Xushu 22," respectively, and 578 miRNAs were co-expressed. The comparison of "Xushu 32" and "Xushu 22" genotypes showed a total of 235 miRNAs with obvious differential expression and 177 salt-responsive miRNAs that were obviously differently expressed between "Xushu 32" and "Xushu 22" under salt stress. The target genes of the miRNAs were predicted and identified using the Target Finder tool and degradome sequencing. The results showed that most of the targets were transcription factors and proteins related to metabolism and stress response. Gene Ontology analysis revealed that these target genes are involved in key pathways related to salt stress response and secondary redox metabolism. The comparative analysis of salt-responsive miRNAs in sweetpotato cultivars with different salt sensitivity is helpful for understanding the regulatory pattern of miRNA in different sweetpotato genotypes and improving the agronomic traits of sweetpotato by miRNA manipulation in the future.
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Affiliation(s)
- Zhengmei Yang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Applied Biology, Chonnam National University, Gwangju, South Korea
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xibin Dai
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Yiliang Wei
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yujie Fang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Qinghe Cao
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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14
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Ma L, Yang Y, Wang Y, Cheng K, Zhou X, Li J, Zhang J, Li R, Zhang L, Wang K, Zeng N, Gong Y, Zhu D, Deng Z, Qu G, Zhu B, Fu D, Luo Y, Zhu H. SlRBP1 promotes translational efficiency via SleIF4A2 to maintain chloroplast function in tomato. THE PLANT CELL 2022; 34:2747-2764. [PMID: 35385118 PMCID: PMC9252502 DOI: 10.1093/plcell/koac104] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/05/2022] [Indexed: 06/01/2023]
Abstract
Many glycine-rich RNA-binding proteins (GR-RBPs) have critical functions in RNA processing and metabolism. Here, we describe a role for the tomato (Solanum lycopersicum) GR-RBP SlRBP1 in regulating mRNA translation. We found that SlRBP1 knockdown mutants (slrbp1) displayed reduced accumulation of total chlorophyll and impaired chloroplast ultrastructure. These phenotypes were accompanied by deregulation of the levels of numerous key transcripts associated with chloroplast functions in slrbp1. Furthermore, native RNA immunoprecipitation-sequencing (nRIP-seq) recovered 61 SlRBP1-associated RNAs, most of which are involved in photosynthesis. SlRBP1 binding to selected target RNAs was validated by nRIP-qPCR. Intriguingly, the accumulation of proteins encoded by SlRBP1-bound transcripts, but not the mRNAs themselves, was reduced in slrbp1 mutants. Polysome profiling followed by RT-qPCR assays indicated that the polysome occupancy of target RNAs was lower in slrbp1 plants than in wild-type. Furthermore, SlRBP1 interacted with the eukaryotic translation initiation factor SleIF4A2. Silencing of SlRBP1 significantly reduced SleIF4A2 binding to SlRBP1-target RNAs. Taking these observations together, we propose that SlRBP1 binds to and channels RNAs onto the SleIF4A2 translation initiation complex and promotes the translation of its target RNAs to regulate chloroplast functions.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Yuqiu Wang
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiwen Zhou
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingyu Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | | | - Lingling Zhang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ni Zeng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yanyan Gong
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Danmeng Zhu
- School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Deng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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15
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ain-Ali QU, Mushtaq N, Amir R, Gul A, Tahir M, Munir F. Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum. PLoS One 2021; 16:e0261215. [PMID: 34914734 PMCID: PMC8675703 DOI: 10.1371/journal.pone.0261215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/27/2021] [Indexed: 12/24/2022] Open
Abstract
Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.
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Affiliation(s)
- Qurat-ul ain-Ali
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Nida Mushtaq
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rabia Amir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Alvina Gul
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Tahir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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16
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Santos Gomes D, de Andrade Silva EM, de Andrade Rosa EC, Silva Gualberto NG, de Jesus Souza MÁ, Santos G, Pirovani CP, Micheli F. Identification of a key protein set involved in Moniliophthora perniciosa necrotrophic mycelium and basidiocarp development. Fungal Genet Biol 2021; 157:103635. [PMID: 34700000 DOI: 10.1016/j.fgb.2021.103635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Moniliophthora perniciosa is a hemibiotrophic fungus that causes witches' broom disease in cacao (Theobroma cacao L.). The biotrophic fungal phase initiates the disease and is characterized by a monokaryotic mycelium, while the necrotrophic phase is characterized by a dikaryotic mycelium and leads to necrosis of infected tissues. A study of the necrotrophic phase was conducted on bran-based solid medium, which is the only medium that enables basidiocarp and basidiospore production. Six different fungal developmental phases were observed according to the mycelium colour or the organ produced: white, yellow, pink, dark pink, primordium and basidiocarp. In this study, we identified notable proteins in each phase, particularly those accumulated prior to basidiocarp formation. Proteins were analysed by proteomics; 2-D gels showed 300-550 spots. Statistically differentially accumulated spots were sequenced by mass spectrometry and 259 proteins were identified and categorized into nine functional classes. Proteins related to energy metabolism, protein folding and morphogenesis that were potentially involved in primordium and basidiocarp formation were identified; these proteins may represent useful candidates for further analysis related to the spread and pathogenesis of this fungus. To the best of our knowledge, this report describes the first proteomic analysis of the developmental phases of Moniliophthora perniciosa.
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Affiliation(s)
- Dayane Santos Gomes
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Edson Mario de Andrade Silva
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Emilly Caroline de Andrade Rosa
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Nina Gabriela Silva Gualberto
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Monaliza Átila de Jesus Souza
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Gesivaldo Santos
- Universidade Estadual do Sudoeste da Bahia (UESB), Av. José Moreira Sobrinho, Jequié, Bahia 45206-190, Brazil
| | - Carlos Priminho Pirovani
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, Km 16, Ilhéus, Bahia 45662-900, Brazil; CIRAD, UMR AGAP, F-34398 Montpellier, France.
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17
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Abdullah-Zawawi MR, Ahmad-Nizammuddin NF, Govender N, Harun S, Mohd-Assaad N, Mohamed-Hussein ZA. Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice. Sci Rep 2021; 11:19678. [PMID: 34608238 PMCID: PMC8490385 DOI: 10.1038/s41598-021-99206-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/21/2021] [Indexed: 01/25/2023] Open
Abstract
Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon–intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.
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Affiliation(s)
| | - Nur-Farhana Ahmad-Nizammuddin
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Nisha Govender
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Sarahani Harun
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Norfarhan Mohd-Assaad
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.,Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
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18
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Tang Y, Huang C, Li Y, Wang Y, Zhang C. Genome-wide identification, phylogenetic analysis, and expression profiling of glycine-rich RNA-binding protein (GRPs) genes in seeded and seedless grapes ( Vitis vinifera). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2231-2243. [PMID: 34744363 PMCID: PMC8526680 DOI: 10.1007/s12298-021-01082-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Glycine-rich RNA-binding proteins (GRPs) are essential for many physiological and biochemical processes in plants, especially the response to environmental stresses. GRPs exist widely in angiosperms and gymnosperms plant species; however, their roles in Vitis vinifera are still poorly understood. To characterize VviGRP gene family, we performed a genomic survey, bioinformatics and expression analysis of VviGRPs in grape. We identified nineteen VviGRPs gene family members. The result of bioinformatics analysis showed their motif distribution, gene structure characteristics and chromosomal locations. Then we carried out synteny and phylogenetic analysis to study the origin and evolutionary relationship of GRPs. Tissue-specific expression analysis showed that VviGRPs have different expression patterns. Meanwhile, we studied expression profiles of seventeen ovule-expressed genes during seed development of stenospermocarpic seedless and seeded grapes, and the result showed that most of them have much higher relative expression levels in stenospermocarpic seedless grapes than that of seeded one before 25 days after full bloom (DAFB). It is suggested that VviGRPs may involve in the seed development process. Taken together, our research indicated that VviGRPs are related to seed development and will be beneficial for further investigations into the seed abortion mechanism under stenospermocarpic grapes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01082-3.
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Affiliation(s)
- Yujin Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Congbo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Yan Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, People’s Republic of China, Yangling, 712100 Shaanxi China
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19
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Ma L, Cheng K, Li J, Deng Z, Zhang C, Zhu H. Roles of Plant Glycine-Rich RNA-Binding Proteins in Development and Stress Responses. Int J Mol Sci 2021; 22:ijms22115849. [PMID: 34072567 PMCID: PMC8198583 DOI: 10.3390/ijms22115849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/02/2023] Open
Abstract
In recent years, much progress has been made in elucidating the functional roles of plant glycine-rich RNA-binding proteins (GR-RBPs) during development and stress responses. Canonical GR-RBPs contain an RNA recognition motif (RRM) or a cold-shock domain (CSD) at the N-terminus and a glycine-rich domain at the C-terminus, which have been associated with several different RNA processes, such as alternative splicing, mRNA export and RNA editing. However, many aspects of GR-RBP function, the targeting of their RNAs, interacting proteins and the consequences of the RNA target process are not well understood. Here, we discuss recent findings in the field, newly defined roles for GR-RBPs and the actions of GR-RBPs on target RNA metabolism.
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Affiliation(s)
- Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Zhiqi Deng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (L.M.); (K.C.); (J.L.); (Z.D.)
- Correspondence:
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20
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Hou F, Du T, Qin Z, Xu T, Li A, Dong S, Ma D, Li Z, Wang Q, Zhang L. Genome-wide in silico identification and expression analysis of beta-galactosidase family members in sweetpotato [Ipomoea batatas (L.) Lam]. BMC Genomics 2021; 22:140. [PMID: 33639840 PMCID: PMC7912918 DOI: 10.1186/s12864-021-07436-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022] Open
Abstract
Background Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant development and environmental stress adaptation. However, the function of bgal genes in sweetpotato remains unclear. Results In this study, 17 β-galactosidase genes (Ibbgal) were identified in sweetpotato, which were classified into seven subfamilies using interspecific phylogenetic and comparative analysis. The promoter regions of Ibbgals harbored several stress, hormone and light responsive cis-acting elements. Quantitative real-time PCR results displayed that Ibbgal genes had the distinct expression patterns across different tissues and varieties. Moreover, the expression profiles under various hormonal treatments, abiotic and biotic stresses were highly divergent in leaves and root. Conclusions Taken together, these findings suggested that Ibbgals might play an important role in plant development and stress responses, which provided evidences for further study of bgal function and sweetpotato breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07436-1.
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Affiliation(s)
- Fuyun Hou
- Key laboratory of phylogeny and comparative genomics of the Jiangsu province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.,Crop research institute, Shandong Academy of Agricultural Sciences/ Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
| | - Taifeng Du
- Key laboratory of phylogeny and comparative genomics of the Jiangsu province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zhen Qin
- Crop research institute, Shandong Academy of Agricultural Sciences/ Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
| | - Tao Xu
- Key laboratory of phylogeny and comparative genomics of the Jiangsu province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Aixian Li
- Crop research institute, Shandong Academy of Agricultural Sciences/ Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
| | - Shunxu Dong
- Crop research institute, Shandong Academy of Agricultural Sciences/ Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
| | - Daifu Ma
- Key laboratory of phylogeny and comparative genomics of the Jiangsu province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Zongyun Li
- Key laboratory of phylogeny and comparative genomics of the Jiangsu province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
| | - Qingmei Wang
- Crop research institute, Shandong Academy of Agricultural Sciences/ Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China
| | - Liming Zhang
- Key laboratory of phylogeny and comparative genomics of the Jiangsu province, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China. .,Crop research institute, Shandong Academy of Agricultural Sciences/ Scientific Observing and Experimental Station of Tuber and Root Crops in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Jinan, 250100, China.
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21
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Sun H, Mei J, Zhao W, Hou W, Zhang Y, Xu T, Wu S, Zhang L. Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato ( Ipomoea batatas). FRONTIERS IN PLANT SCIENCE 2021; 12:801061. [PMID: 35126426 PMCID: PMC8815303 DOI: 10.3389/fpls.2021.801061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 05/11/2023]
Abstract
As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in "regulation of root morphogenesis," "cell division," "cytoskeleton organization," and "plant-type cell wall organization or biogenesis," indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.
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Affiliation(s)
- Haoyun Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingzhao Mei
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tao Xu,
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Shaoyuan Wu,
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Lei Zhang,
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22
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Chandra AK, Pandey D, Tiwari A, Sharma D, Agarwal A, Sood S, Kumar A. An Omics Study of Iron and Zinc Homeostasis in Finger Millet: Biofortified Foods for Micronutrient Deficiency in an Era of Climate Change? ACTA ACUST UNITED AC 2020; 24:688-705. [DOI: 10.1089/omi.2020.0095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ajay Kumar Chandra
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Apoorv Tiwari
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad, India
| | - Divya Sharma
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Botany, Delhi University, Delhi, India
| | - Aparna Agarwal
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Salej Sood
- Department of Crop Improvement, Central Potato Research Institute, Shimla, India
| | - Anil Kumar
- Director of Education, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
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23
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Lu X, Cheng Y, Gao M, Li M, Xu X. Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). Front Genet 2020; 11:774. [PMID: 32849790 PMCID: PMC7396569 DOI: 10.3389/fgene.2020.00774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/30/2020] [Indexed: 11/15/2022] Open
Abstract
Plant Glycine-rich proteins (GRP), a superfamily with a glycine-rich domain, play an important role in various stresses such as high or low temperature stress and drought stress. GRP genes have been studied in many plants, but seldom in Chinese cabbage (Brassica rapa L. ssp. pekinensis). In this study, a total of 64 GRP genes were identified in Chinese cabbage by homology comparative analysis. The physical and chemical characteristics predicted by ProtParam tool revealed that 62.5% of BrGRPs were alkaline, 53.1% were stable, and 79.7% were hydrophilic. Conserved domain analysis by MEME and TBtools showed that 64 BrGRPs contained 20 of the same conserved motifs, based on which BrGRPs were classified into five main classes and four subclasses in class IV to clarify their evolutionary relationship. Our results demonstrated that The BrGRP genes were located on ten chromosomes and in three different subgenomes of Chinese cabbage, and 43 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the transcriptome data, 64 BrGRP genes showed abnormal expression under high temperature stress, 52 under low temperature stress, 39 under drought stress, and 23 responses to soft rot. A large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE were found in their promoter regions by PlantCare, which corresponded with differential expressions. Two BrGRP genes-w546 (Bra030284) and w1409 (Bra014000), both belonging to the subfamily Subclass IVa RBP-GRP (RNA binding protein-glycine rich protein), were up-regulated under 150 mmol⋅L-1 NaCl stress in Chinese cabbage. However, the overexpressed w546 gene could significantly inhibit seed germination, while w1409 significantly accelerated seed germination under 100 mmol⋅L-1 NaCl or 300 mmol⋅L-1 mannitol stresses. In short, most BrGRP genes showed abnormal expression under adversity stress, and some were involved in multiple stress responses, suggesting a potential capacity to resist multiple biotic and abiotic stresses, which is worthy of further study. Our study provides a systematic investigation of the molecular characteristics and expression patterns of BrGRP genes and promotes for further work on improving stress resistance of Chinese cabbage.
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Affiliation(s)
| | | | | | | | - Xiaoyong Xu
- College of Horticulture, Shanxi Agricultural University; and Collaborative Innovation Center for Improving Quality and Increasing Profits of Protected Vegetables in Shanxi, Taigu, China
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24
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Belay ZA, Caleb OJ, Vorster A, van Heerden C, Opara UL. Transcriptomic changes associated with husk scald incidence on pomegranate fruit peel during cold storage. Food Res Int 2020; 135:109285. [PMID: 32527480 DOI: 10.1016/j.foodres.2020.109285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
Pomegranate fruit is valued for its social, economic, aesthetic and health benefits. The fruit rapidly loses quality after harvest due to continued metabolic responses and physiological disorders under sub-optimal conditions. The incidence of physiological disorder such as husk scald manifests during storage and commercial shipping, which affects the appearance and limits marketability. Despite the importance of pomegranate husk scald, little information is available about the origin and molecular mechanisms. Therefore, the aim of this study was to investigate the scald incidence of pomegranate fruit at molecular level using RNA-Seq (Ion Proton™ Next Generation Sequencing) by analyzing peel transcriptomic changes. The RNA-seq analysis generated 98,441,278 raw reads. 652 Differentially Expressed Genes (DEGs) with a fold change of > |2|, a p value ≤ 0.05 and a false discovery rate (FDR) of <0.05 were identified between healthy and scald fruit peels. An analysis of the gene ontologies of these DEGs revealed the 432 genes were assigned with molecular functions, 272 as cellular components and 205 as part of biological processes. In this analysis, genes (Pgr023188 and Pgr025081) that encode uncharacterized protein and gene (Pgr007593) that encodes glycosyltransferase showed significantly highest fold changes. Genes (Pgr003448, Pgr006024 and Pgr023696) involved in various iron binding and oxidoreductase activities were significantly suppressed. This is the first transcriptome analysis of pomegranate fruit peel related to husk scald development. Results obtained from this study will add valuable information on husk scald related changes on pomegranate fruit at genomic level and provide insight on other related physiological disorders.
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Affiliation(s)
- Zinash A Belay
- Postharvest Technology Research Laboratory, South African Research Chair in Postharvest Technology, Department of Horticultural Science, Faculty of AgriSciences, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Oluwafemi J Caleb
- Agri-Food Systems and Omics Laboratory, Post-Harvest and Agro-Processing Technologies (PHATs), Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Alvera Vorster
- The Central Analytical Facilities (CAF), The DNA-sequencing Unit, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Carel van Heerden
- The Central Analytical Facilities (CAF), The DNA-sequencing Unit, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Umezuruike Linus Opara
- Postharvest Technology Research Laboratory, South African Research Chair in Postharvest Technology, Department of Horticultural Science, Faculty of AgriSciences, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa.
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25
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Yang Z, Zhu P, Kang H, Liu L, Cao Q, Sun J, Dong T, Zhu M, Li Z, Xu T. High-throughput deep sequencing reveals the important role that microRNAs play in the salt response in sweet potato (Ipomoea batatas L.). BMC Genomics 2020; 21:164. [PMID: 32066373 PMCID: PMC7027035 DOI: 10.1186/s12864-020-6567-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/07/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industrial crop that ranks seventh in staple food production. However, the regulatory mechanism of miRNA-mediated abiotic stress response in sweet potato remains unclear. RESULTS In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed sweet potato cultivars and its untreated control. Twelve small non-coding RNA libraries from NaCl-free (CK) and NaCl-treated (Na150) sweet potato leaves and roots were constructed for salt-responsive miRNA identification in sweet potatoes. A total of 475 known miRNAs (belonging to 66 miRNA families) and 175 novel miRNAs were identified. Among them, 51 (22 known miRNAs and 29 novel miRNAs) were significantly up-regulated and 76 (61 known miRNAs and 15 novel miRNAs) were significantly down-regulated by salinity stress in sweet potato leaves; 13 (12 known miRNAs and 1 novel miRNAs) were significantly up-regulated and 9 (7 known miRNAs and 2 novel miRNAs) were significantly down-regulated in sweet potato roots. Furthermore, 636 target genes of 314 miRNAs were validated by degradome sequencing. Deep sequencing results confirmed by qRT-PCR experiments indicated that the expression of most miRNAs exhibit a negative correlation with the expression of their targets under salt stress. CONCLUSIONS This study provides insights into the regulatory mechanism of miRNA-mediated salt response and molecular breeding of sweet potatoes though miRNA manipulation.
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Affiliation(s)
- Zhengmei Yang
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Panpan Zhu
- 0000 0001 0356 9399grid.14005.30Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 South Korea
| | - Hunseung Kang
- 0000 0001 0356 9399grid.14005.30Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757 South Korea
| | - Lin Liu
- 0000 0001 0472 9649grid.263488.3Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Qinghe Cao
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121 Jiangsu China
| | - Jian Sun
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Tingting Dong
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Mingku Zhu
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Zongyun Li
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
| | - Tao Xu
- 0000 0000 9698 6425grid.411857.eKey Lab of Phylogeny and Comparative Genomics of the Jiangsu Province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116 Jiangsu Province China
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26
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Genome-wide identification and characterization of late embryogenesis abundant protein-encoding gene family in wheat: Evolution and expression profiles during development and stress. Gene 2020; 736:144422. [PMID: 32007584 DOI: 10.1016/j.gene.2020.144422] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Late embryogenesis abundant (LEA) proteins are involved in plant stress responses and osmotic regulation, and they are accumulated in the late embryonic stage. There have been no previous genome-wide analyses of the LEA gene family members in wheat and its close relatives. In this study, 281, 53, 151, 89, 99, and 99 LEA genes were identified in wheat (Triticum aestivum), Triticum urartu, Triticum dicoccoides, Aegilops tauschii, barley, and Brachypodium distachyon, respectively. The wheat LEA gene family (TaLEA genes) was divided into eight subfamilies according to the conserved domains. All TaLEA genes contain very few introns (<3) and they are unevenly distributed on the 21 chromosomes. We identified 39 pairs of tandem duplication genes and 9 pairs of segmental duplication genes in the wheat LEA gene family. This proved that the tandem duplication and segmental duplication played an important role in the expansion of the TaLEA gene family. According to published transcriptome data and qRT-PCR analysis, the TaLEA genes exhibit different tissue expression patterns and they are regulated by various abiotic stresses, especially salt and cold stress. This study provides a comprehensive understanding of the wheat LEA gene family.
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Wan R, Liu J, Yang Z, Zhu P, Cao Q, Xu T. Genome-wide identification, characterisation and expression profile analysis of DEAD-box family genes in sweet potato wild ancestor Ipomoea trifida under abiotic stresses. Genes Genomics 2020; 42:325-335. [DOI: 10.1007/s13258-019-00910-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022]
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28
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Wang M, Zang L, Jiao F, Perez-Garcia MD, Ogé L, Hamama L, Le Gourrierec J, Sakr S, Chen J. Sugar Signaling and Post-transcriptional Regulation in Plants: An Overlooked or an Emerging Topic? FRONTIERS IN PLANT SCIENCE 2020; 11:578096. [PMID: 33224165 PMCID: PMC7674178 DOI: 10.3389/fpls.2020.578096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/02/2020] [Indexed: 05/21/2023]
Abstract
Plants are autotrophic organisms that self-produce sugars through photosynthesis. These sugars serve as an energy source, carbon skeletons, and signaling entities throughout plants' life. Post-transcriptional regulation of gene expression plays an important role in various sugar-related processes. In cells, it is regulated by many factors, such as RNA-binding proteins (RBPs), microRNAs, the spliceosome, etc. To date, most of the investigations into sugar-related gene expression have been focused on the transcriptional level in plants, while only a few studies have been conducted on post-transcriptional mechanisms. The present review provides an overview of the relationships between sugar and post-transcriptional regulation in plants. It addresses the relationships between sugar signaling and RBPs, microRNAs, and mRNA stability. These new items insights will help to reach a comprehensive understanding of the diversity of sugar signaling regulatory networks, and open onto new investigations into the relevance of these regulations for plant growth and development.
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Affiliation(s)
- Ming Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Lili Zang
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | | | - Laurent Ogé
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Latifa Hamama
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - José Le Gourrierec
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
| | - Soulaiman Sakr
- IRHS-UMR1345, INRAE, Institut Agro, SFR 4207 QuaSaV, Université d’Angers, Beaucouzé, France
- Soulaiman Sakr,
| | - Jingtang Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Jingtang Chen,
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Li Y, Zhang L, Zhu P, Cao Q, Sun J, Li Z, Xu T. Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses. BMC Genet 2019; 20:90. [PMID: 31795942 PMCID: PMC6889533 DOI: 10.1186/s12863-019-0789-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato. RESULTS A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses. CONCLUSIONS In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.
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Affiliation(s)
- Yuxia Li
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Lei Zhang
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Panpan Zhu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, South Korea
| | - Qinghe Cao
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121, Jiangsu, China
| | - Jian Sun
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Zongyun Li
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
| | - Tao Xu
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
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Chen Y, Zhu P, Wu S, Lu Y, Sun J, Cao Q, Li Z, Xu T. Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida. BMC Genomics 2019; 20:911. [PMID: 31783728 PMCID: PMC6884806 DOI: 10.1186/s12864-019-6316-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/21/2019] [Indexed: 11/22/2022] Open
Abstract
Background GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China. However, the function of sweet potato GRAS genes remains unknown. Results In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses. Conclusions Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.
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Affiliation(s)
- Yao Chen
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Panpan Zhu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, South Korea
| | - Shaoyuan Wu
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Yan Lu
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Jian Sun
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Qinghe Cao
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, Xuzhou, 221121, Jiangsu, China
| | - Zongyun Li
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China.
| | - Tao Xu
- Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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Pinto RT, Freitas NC, Máximo WPF, Cardoso TB, Prudente DDO, Paiva LV. Genome-wide analysis, transcription factor network approach and gene expression profile of GH3 genes over early somatic embryogenesis in Coffea spp. BMC Genomics 2019; 20:812. [PMID: 31694532 PMCID: PMC6836404 DOI: 10.1186/s12864-019-6176-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/07/2019] [Indexed: 01/25/2023] Open
Abstract
Background Coffee production relies on plantations with varieties from Coffea arabica and Coffea canephora species. The first, the most representative in terms of coffee consumption, is mostly propagated by seeds, which leads to management problems regarding the plantations maintenance, harvest and processing of grains. Therefore, an efficient clonal propagation process is required for this species cultivation, which is possible by reaching a scalable and cost-effective somatic embryogenesis protocol. A key process on somatic embryogenesis induction is the auxin homeostasis performed by Gretchen Hagen 3 (GH3) proteins through amino acid conjugation. In this study, the GH3 family members were identified on C. canephora genome, and by performing analysis related to gene and protein structure and transcriptomic profile on embryogenic tissues, we point a GH3 gene as a potential regulator of auxin homeostasis during early somatic embryogenesis in C. arabica plants. Results We have searched within the published C. canephora genome and found 17 GH3 family members. We checked the conserved domains for GH3 proteins and clustered the members in three main groups according to phylogenetic relationships. We identified amino acids sets in four GH3 proteins that are related to acidic amino acid conjugation to auxin, and using a transcription factor (TF) network approach followed by RT-qPCR we analyzed their possible transcriptional regulators and expression profiles in cells with contrasting embryogenic potential in C. arabica. The CaGH3.15 expression pattern is the most correlated with embryogenic potential and with CaBBM, a C. arabica ortholog of a major somatic embryogenesis regulator. Conclusion Therefore, one out of the GH3 members may be influencing on coffee somatic embryogenesis by auxin conjugation with acidic amino acids, which leads to the phytohormone degradation. It is an indicative that this gene can serve as a molecular marker for coffee cells with embryogenic potential and needs to be further studied on how much determinant it is for this process. This work, together with future studies, can support the improvement of coffee clonal propagation through in vitro derived somatic embryos.
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Affiliation(s)
- Renan Terassi Pinto
- Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil
| | | | | | | | | | - Luciano Vilela Paiva
- Department of Chemistry, Federal University of Lavras, Lavras, MG, 37200000, Brazil.
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Zamora-Briseño JA, Pereira-Santana A, Reyes-Hernández SJ, Castaño E, Rodríguez-Zapata LC. Global Dynamics in Protein Disorder during Maize Seed Development. Genes (Basel) 2019; 10:genes10070502. [PMID: 31262071 PMCID: PMC6678312 DOI: 10.3390/genes10070502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Intrinsic protein disorder is a physicochemical attribute of some proteins lacking tridimensional structure and is collectively known as intrinsically disordered proteins (IDPs). Interestingly, several IDPs have been associated with protective functions in plants and with their response to external stimuli. To correlate the modulation of the IDPs content with the developmental progression in seed, we describe the expression of transcripts according to the disorder content of the proteins that they codify during seed development, from the early embryogenesis to the beginning of the desiccation tolerance acquisition stage. We found that the total expression profile of transcripts encoding for structured proteins is highly increased during middle phase. However, the relative content of protein disorder is increased as seed development progresses. We identified several intrinsically disordered transcription factors that seem to play important roles throughout seed development. On the other hand, we detected a gene cluster encoding for IDPs at the end of the late phase, which coincides with the beginning of the acquisition of desiccation tolerance. In conclusion, the expression pattern of IDPs is highly dependent on the developmental stage, and there is a general reduction in the expression of transcripts encoding for structured proteins as seed development progresses. We proposed maize seeds as a model to study the regulation of protein disorder in plant development and its involvement in the acquisition of desiccation tolerance in plants.
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Affiliation(s)
- Jesús Alejandro Zamora-Briseño
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del estado de Jalisco. División de Biotecnología Industrial. Camino Arenero 1227, El Bajío, Zapopan, Jalisco. C.P. 45019
| | - Sandi Julissa Reyes-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México
| | - Luis Carlos Rodríguez-Zapata
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43, número 130, Chuburná de Hidalgo, CP 97205, Mérida, Yucatán, México.
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Yang Z, Sun J, Chen Y, Zhu P, Zhang L, Wu S, Ma D, Cao Q, Li Z, Xu T. Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida. BMC Genet 2019; 20:41. [PMID: 31023242 PMCID: PMC6482516 DOI: 10.1186/s12863-019-0743-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/04/2019] [Indexed: 01/02/2023] Open
Abstract
Background The basic leucine zipper (bZIP) transcription factor is one of the most abundant and conserved transcription factor families. In addition to being involved in growth and development, bZIP transcription factors also play an important role in plant adaption to abiotic stresses. Results A total of 41 bZIP genes that encode 66 proteins were identified in Ipomoea trifida. They were distributed on 14 chromosomes of Ipomoea trifida. Segmental and tandem duplication analysis showed that segmental duplication played an important role in the ItfbZIP gene amplification. ItfbZIPs were divided into ten groups (A, B, C, D, E, F, G, H, I and S groups) according to their phylogenetic relationships with Solanum lycopersicum and Arabidopsis thaliana. The regularity of the exon/intron numbers and distributions is consistent with the group classification in evolutionary tree. Prediction of the cis-acting elements found that promoter regions of ItfbZIPs harbored several stress responsive cis-acting elements. Protein three-dimensional structural analysis indicated that ItfbZIP proteins mainly consisted of α-helices and random coils. The gene expression pattern from transcriptome data and qRT-PCR analysis showed that ItfbZIP genes expressed with a tissue-specific manner and differently expressed under various abiotic stresses, suggesting that the ItfbZIPs were involved in stress response and adaption in Ipomoea trifida. Conclusions Genome-wide identification, gene structure, phylogeny and expression analysis of bZIP gene in Ipomoea trifida supplied a solid theoretical foundation for the functional study of bZIP gene family and further facilitated the molecular breeding of sweet potato. Electronic supplementary material The online version of this article (10.1186/s12863-019-0743-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhengmei Yang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Jian Sun
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Yao Chen
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Panpan Zhu
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 500-757, South Korea
| | - Lei Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Shaoyuan Wu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Daifu Ma
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121, Jiangsu, China
| | - Qinghe Cao
- Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, CAAS, Xuzhou, 221121, Jiangsu, China
| | - Zongyun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China. .,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
| | - Tao Xu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China. .,Key lab of phylogeny and comparative genomics of the Jiangsu province, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
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